15101
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Molecular Dynamics Simulations: The Limits and Beyond. COMPUTATIONAL MOLECULAR DYNAMICS: CHALLENGES, METHODS, IDEAS 1999. [DOI: 10.1007/978-3-642-58360-5_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15102
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Darden T, Pearlman D, Pedersen LG. Ionic charging free energies: Spherical versus periodic boundary conditions. J Chem Phys 1998. [DOI: 10.1063/1.477788] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15103
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Samuelson SO, Martyna GJ. Two dimensional umbrella sampling techniques for the computer simulation study of helical peptides at thermal equilibrium: The 3K(I) peptidein vacuoand solution. J Chem Phys 1998. [DOI: 10.1063/1.477795] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15104
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Weber W, Demirdjian H, Lins RD, Briggs JM, Ferreira R, McCammon JA. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn 1998; 16:733-45. [PMID: 10052629 DOI: 10.1080/07391102.1998.10508285] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The three-dimensional structure of the active site region of the enzyme HIV-1 integrase is not unambiguously known. This region includes a flexible peptide loop that cannot be well resolved in crystallographic determinations. Here we present two different computational approaches with different levels of resolution and on different time-scales to understand this flexibility and to analyze the dynamics of this part of the protein. We have used molecular dynamics simulations with an atomic model to simulate the region in a realistic and reliable way for 1 ns. It is found that parts of the loop wind up after 300 ps to extend an existing helix. This indicates that the helix is longer than in the earlier crystal structures that were used as basis for this study. Very recent crystal data confirms this finding, underlining the predictive value of accurate MD simulations. Essential dynamics analysis of the MD trajectory yields an anharmonic motion of this loop. We have supplemented the MD data with a much lower resolution Brownian dynamics simulation of 600 ns length. It provides ideas about the slow-motion dynamics of the loop. It is found that the loop explores a conformational space much larger than in the MD trajectory, leading to a "gating"-like motion with respect to the active site.
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Affiliation(s)
- W Weber
- Department of Pharmacology, University of California, San Diego, La Jolla 92093-0365, USA
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15105
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Srinivasan J, Miller J, Kollman PA, Case DA. Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn 1998; 16:671-82. [PMID: 10052623 DOI: 10.1080/07391102.1998.10508279] [Citation(s) in RCA: 191] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We apply continuum solvent models to investigate the relative stability of various conformational forms for two RNA sequences, GGAC(UUCG)GUCC and GGUG(UGAA)CACC. In the first part, we compare alternate hairpin conformations to explore the reliability of these models to discriminate between different local conformations. A second part looks at the hairpin-duplex conversion for the UUCG sequence, identifying major contributors to the thermodynamics of a much large scale transition. Structures were taken as snapshots from multi-nanosecond molecular dynamics simulations computed in a consistent fashion using explicit solvent and with long-range electrostatics accounted for using the Particle-Mesh Ewald procedure. The electrostatic contribution to solvation energies were computed using both a finite-difference Poisson-Boltzmann (PB) model and a pairwise Generalized Born model; non-electrostatic contributions were estimated with a surface-area dependent term. To these solvation free energies were added the mean solute internal energies (determined from a molecular mechanics potential) and estimates of the solute entropy (from a harmonic analysis). Consistent with experiment and with earlier solvated molecular dynamics simulations, the UUCG hairpin was found to prefer conformers close to a recent NMR structure determination in preference to those from an earlier NMR study. Similarly, results for the UGAA hairpin favored an NMR-derived structure over that to be expected for a generic GNRA hairpin loop. Experimental free energies are not known for the hairpin/duplex conversion, but must be close to zero since hairpins are seen in solution and duplexes in crystals; out calculations find a value near zero and illustrate the expected interplay of solvation, salt effects and entropy in affecting this equilibrium.
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Affiliation(s)
- J Srinivasan
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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15106
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Deserno M, Holm C. How to mesh up Ewald sums. II. An accurate error estimate for the particle–particle–particle-mesh algorithm. J Chem Phys 1998. [DOI: 10.1063/1.477415] [Citation(s) in RCA: 232] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15107
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Deserno M, Holm C. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J Chem Phys 1998. [DOI: 10.1063/1.477414] [Citation(s) in RCA: 498] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15108
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Soliva R, Laughton CA, Luque FJ, Orozco M. Molecular Dynamics Simulations in Aqueous Solution of Triple Helices Containing d(G·C·C) Trios. J Am Chem Soc 1998. [DOI: 10.1021/ja981121q] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Robert Soliva
- Contribution from the Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Marti i Franques 1, Barcelona 08028, Spain, Cancer Research Laboratories, Department of Pharmaceutical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal sn, Barcelona 08028, Spain
| | - Charles A. Laughton
- Contribution from the Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Marti i Franques 1, Barcelona 08028, Spain, Cancer Research Laboratories, Department of Pharmaceutical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal sn, Barcelona 08028, Spain
| | - F. Javier Luque
- Contribution from the Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Marti i Franques 1, Barcelona 08028, Spain, Cancer Research Laboratories, Department of Pharmaceutical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal sn, Barcelona 08028, Spain
| | - Modesto Orozco
- Contribution from the Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Marti i Franques 1, Barcelona 08028, Spain, Cancer Research Laboratories, Department of Pharmaceutical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal sn, Barcelona 08028, Spain
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15109
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Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998; 282:740-4. [PMID: 9784131 DOI: 10.1126/science.282.5389.740] [Citation(s) in RCA: 922] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.
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Affiliation(s)
- Y Duan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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15110
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Bonvin AM, Sunnerhagen M, Otting G, van Gunsteren WF. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. J Mol Biol 1998; 282:859-73. [PMID: 9743632 DOI: 10.1006/jmbi.1998.2034] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure and hydration of the DNA duplex d-(AGCGTACTAGTACGCT)2 corresponding to the trp operator fragment used in the crystal structure of the half site complex (PDB entry 1TRR) was studied by a 1.4 ns molecular dynamics simulation in water. The simulation, starting from a B-DNA conformation, used a non-bonded cutoff of 1.4 nm with a reaction field correction and resulted in a stable trajectory. The average DNA conformation obtained was closer to the ones found in the crystal structures of the complexes (PDB entries 1TRO and 1TRR) than to the crystal structure of unbound trp operator (Nucleic Acid Database entry BDJ061). The DNA hydration was characterized in terms of hydrogen bond percentages and corresponding residence times. The residence times of water molecules within 0.35 nm of the DNA non-exchangeable protons were calculated for comparison with NMR measurements of intermolecular water-DNA NOEs and nuclear magnetic relaxation dispersion measurements. No significant difference was found between major and minor groove hydration. The DNA donors and acceptors were hydrogen bonded to water molecules for 77(+/-19)% of the time on average. The average residence time of the hydrogen bonded water molecules was 11(+/-11) ps with a maximum of 223 ps. When all water molecules within NOE distance (0.35 nm) of non-exchangeable protons were considered, the average residence times increased to an average of 100(+/-4) ps and a maximum of 608 ps. These results agree with the experimental NMR results of Sunnerhagen et al. which did not show any evidence for water molecules bound with more than 1 ns residence time on the DNA surface. The exchange of hydration water from the DNA occurred in the major groove primarily through direct exchange with the bulk solvent, while access to and from the minor groove frequently proceeded via pathways involving ribose O3' and O4' and phosphate O2P oxygen atoms. The most common water diffusion pathways in the minor groove were perpendicular to the groove direction. In general, water molecules visited only a limited number of sites in the DNA grooves before exiting. The hydrogen bonding sites, where hydrogen bonds could be formed with donor and acceptor groups of the DNA, were filled with water molecules with an average B-factor value of 0.58 mn2. No special values were observed at any of the sites, where water molecules were observed both in the trp repressor/operator co-crystals and in the crystal structure of unbound DNA.
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Affiliation(s)
- A M Bonvin
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, CH-8092, Switzerland
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15111
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15112
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Cheatham TE, Srinivasan J, Case DA, Kollman PA. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J Biomol Struct Dyn 1998; 16:265-80. [PMID: 9833666 DOI: 10.1080/07391102.1998.10508245] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Molecular dynamics simulation in explicit solvent and continuum solvent models are applied to investigate the relative stability of A- and B-form helices for two DNA sequences, dA10-dT10 and dG10-dC10 in three structural forms. One structural form is based on an unrestrained molecular dynamics (MD) trajectory starting from a canonical B-DNA structure, the second is based on a MD trajectory starting in a canonical B-DNA structure with the sugars constrained to be C2'-endo and the third simulation started from a canonical A-DNA structure with the sugars constrained to C3'-endo puckers. For the energetic analysis, structures were taken as snapshots from nanosecond length molecular dynamics simulations computed in a consistent fashion in explicit solvent, applying the particle mesh Ewald method and the Cornell et al. force field. The electrostatic contributions to solvation free energies are computed using both a finite-difference Poisson-Boltzmann model and a pairwise Generalized Born model. The non-electrostatic contributions to the solvation free energies are estimated with a solvent accessible surface area dependent term. To estimate the gas phase component of the relative free energy between the various structures, the mean solute internal energies (determined with the Cornell et al. molecular mechanics potential including all pairwise interactions within the solute) and estimates of the solute entropy (using a harmonic approximation) were used. Consistent with experiment, the polyG-polyC (GC) structures are found to be much more A-phillic than the polyA-polyT (AT) structures, the latter being quite A-phobic. The dominant energy components responsible for this difference comes from the internal and van der Waal energies. A perhaps less appreciated difference between the GC and AT rich sequences is suggested by the calculated salt dependence which demonstrates a significantly enhanced ability to drive GC rich sequences towards an A-form structure compared to AT rich sequences. In addition to being A-phobic, the AT structure also has a noticably larger helical repeat than GC and other mixed sequence duplexes, consistent with experiment. Analysis of the average solvent density from the trajectories shows hydration patterns in qualitative agreement with experiment and previous theoretical treatments.
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Affiliation(s)
- T E Cheatham
- Laboratory of Biophysical Chemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-5626, USA.
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15113
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Marchi M, Procacci P. Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble. J Chem Phys 1998. [DOI: 10.1063/1.477136] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15114
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Abstract
Computational models of proton binding can range from the chemically complex and statistically simple (as in the quantum calculations) to the chemically simple and statistically complex. Much progress has been made in the multiple-site titration problem. Calculations have improved with the inclusion of more flexibility in regard to both the geometry of the proton binding and the larger scale protein motions associated with titration. This article concentrated on the principles of current calculations, but did not attempt to survey their quantitative performance. This is (1) because such comparisons are given in the cited papers and (2) because continued developments in understanding conformational flexibility and interaction energies will be needed to develop robust methods with strong predictive power. Nevertheless, the advances achieved over the past few years should not be underestimated: serious calculations of protonation behavior and its coupling to conformational change can now be confidently pursued against a backdrop of increasing understanding of the strengths and limitations of such models. It is hoped that such theoretical advances will also spur renewed experimental interest in measuring both overall titration curves and individual pKa values or pKa shifts. Exploration of the shapes of individual titration curves (as measured by Hill coefficients and other parameters) would also be useful in assessing the accuracy of computations and in drawing connections to functional behavior.
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Affiliation(s)
- P Beroza
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
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15115
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Höchtl P, Boresch S, Bitomsky W, Steinhauser O. Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters. J Chem Phys 1998. [DOI: 10.1063/1.477104] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15116
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Torres RA, Bruice TC. Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction. Proc Natl Acad Sci U S A 1998; 95:11077-82. [PMID: 9736692 PMCID: PMC21598 DOI: 10.1073/pnas.95.19.11077] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have performed molecular dynamics (MD) calculations by using one of the recently solved crystal structures of a hammerhead ribozyme. By rotating the alpha, beta, gamma, delta, epsilon, and zeta torsion angles of the phosphate linkage of residue 17, the nucleobase at the cleavage site was slightly rotated out of the active site toward the solution. Unconstrained MD simulations exceeding 1 ns were performed on this starting structure solvated in water with explicit counter ions and two Mg2+ ions at the active site. Our results reveal that near attack conformations consistently were formed in the simulation. These near attack conformations are characterized by assumption of the 2'-hydroxyl to a near in-line position for attack on the -O-(PO2-)-O- phosphorous. Also during the time course of the MD study, one Mg2+ moved immediately to associate with a pro-R phosphate oxygen in the conserved core region, and the second Mg2+ remained associated with the pro-R oxygen on the phosphate linkage undergoing hydrolysis. These results are in accord with a one-metal ion mechanism of catalysis and give insight into the possible roles of many of the conserved residues in the ribozyme.
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Affiliation(s)
- R A Torres
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
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15117
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Lobaskin V, Linse P. Accurate simulation of highly asymmetric electrolytes with charge asymmetry 20:1 and 20:2. J Chem Phys 1998. [DOI: 10.1063/1.476948] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15118
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Duan Y, Wang L, Kollman PA. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci U S A 1998; 95:9897-902. [PMID: 9707572 PMCID: PMC21433 DOI: 10.1073/pnas.95.17.9897] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of magnitude longer than previously reported and will soon enable such simulations to be carried into the microsecond time range. We have used this approach to study the folding of the villin headpiece subdomain, a 36-residue small protein consisting of three helices, from an unfolded structure to a molten globule state, which has a number of features of the native structure. The time development of the solvation free energy, the radius of gyration, and the mainchain rms difference from the native NMR structure showed that the process can be seen as a 60-nsec "burst" phase followed by a slow "conformational readjustment" phase. We found that the burial of the hydrophobic surface dominated the early phase of the folding process and appeared to be the primary driving force of the reduction in the radius of gyration in that phase.
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Affiliation(s)
- Y Duan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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15119
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Hummer G, Gro/nbech-Jensen N, Neumann M. Pressure calculation in polar and charged systems using Ewald summation: Results for the extended simple point charge model of water. J Chem Phys 1998. [DOI: 10.1063/1.476834] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15120
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Strahan GD, Keniry MA, Shafer RH. NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations. Biophys J 1998; 75:968-81. [PMID: 9675197 PMCID: PMC1299770 DOI: 10.1016/s0006-3495(98)77585-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The solution structure and dynamical properties of the potassium-stabilized, hairpin dimer quadruplex formed by the oligonucleotide d(G3T4G3) have been elucidated by a combination of high-resolution NMR and molecular dynamics simulations. Refinement calculations were carried out both in vacuo, without internally coordinated K+ cations, and in explicit water, with internally coordinated K+ cations. In the latter case, the electrostatic interactions were calculated using the particle mesh Ewald (PME) method. The NMR restraints indicate that the K+ quadruplex has a folding arrangement similar to that formed by the same oligonucleotide in the presence of sodium, but with significant local differences. Unlike the Na+ quadruplex, the thymine loops found in K+ exhibit considerable flexibility, and appear to interconvert between two preferred conformations. Furthermore, the NMR evidence points toward K+-stabilized guanine quartets of slightly larger diameter relative to the Na+-stabilized structure. The characteristics of the quartet stem are greatly affected by the modeling technique employed: caged cations alter the size and symmetry of the quartets, and explicit water molecules form hydration spines within the grooves. These results provide insight into those factors that determine the overall stability of hairpin dimer quadruplexes and the effects of different cations in modulating the relative stability of the dimeric hairpin and linear, four-stranded, quadruplex forms.
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Affiliation(s)
- G D Strahan
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
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15121
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Armen RS, Uitto OD, Feller SE. Phospholipid component volumes: determination and application to bilayer structure calculations. Biophys J 1998; 75:734-44. [PMID: 9675175 PMCID: PMC1299748 DOI: 10.1016/s0006-3495(98)77563-0] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.
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Affiliation(s)
- R S Armen
- Department of Chemistry, Whitman College, Walla Walla, Washington 99362 USA
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15122
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Tazaki K, Shimizu K. Molecular Dynamics Simulations in Aqueous Solution: Application to Free Energy Calculation of Oligopeptides. J Phys Chem B 1998. [DOI: 10.1021/jp9803788] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Koichi Tazaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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15123
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Lim A, Saderholm MJ, Makhov AM, Kroll M, Yan Y, Perera L, Griffith JD, Erickson BW. Engineering of betabellin-15D: a 64 residue beta sheet protein that forms long narrow multimeric fibrils. Protein Sci 1998; 7:1545-54. [PMID: 9684887 PMCID: PMC2144068 DOI: 10.1002/pro.5560070708] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The betabellin target structure is a beta-sandwich protein consisting of two 32 residue beta-sheets packed against one another by interaction of their hydrophobic faces. The 32 residue chain of betabellin-15S (HSLTAKIpkLTFSIAphTYTCAV pkYTAKVSH, where p=DPro, k=DLys, and h=DHis) did not fold in water at pH 6.5. Air oxidation of betabellin-15S provided betabellin-15D, the 64 residue disulfide bridged two-chain molecule, which also remained unfolded in water at pH 6.5. By circular dichroic spectropolarimetry, the extent of beta structure observed for betabellin-15D increased with the pH and ionic strength of the solution and the betabellin-15D concentration. By electron microscopy, in 5.0 mM MOPS and 0.25 M NaCl at pH 6.9, betabellin-15D formed long narrow multimeric fibrils. A molecular model was constructed to show that the dimensions of these betabellin-15D fibrils are consistent with a single row of beta-sandwich molecules joined by multiple intersheet H-bonds.
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Affiliation(s)
- A Lim
- Department of Chemistry, The University of North Carolina at Chapel Hill, 27599-3290, USA
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15124
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Chen Z, Blandl T, Prorok M, Warder SE, Li L, Zhu Y, Pedersen LG, Ni F, Castellino FJ. Conformational changes in conantokin-G induced upon binding of calcium and magnesium as revealed by NMR structural analysis. J Biol Chem 1998; 273:16248-58. [PMID: 9632684 DOI: 10.1074/jbc.273.26.16248] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The apo- and metal-bound solution conformations of synthetic conantokin-G (con-G, G1Egamma gammaL5Q gamma NQgamma 10LIRgamma K15SN-CONH2, gamma = gamma-carboxyglutamic acid), an antagonist of N-methyl-D-aspartate receptor-derived neuronal ion channels, have been examined by one- and two-dimensional 1H NMR at neutral pH. A complete structure for the Mg2+-loaded peptide was defined by use of distance geometry calculations and was found to exist as an alpha-helix that spans the entire peptide. The alpha-helical nature of Mg2+/con-G was also supported by the small values (<5.5 Hz) of the 3JHNalpha coupling constants measured for amino acid residues 3-5, 8, 9, and 11-16, and the small values (<4 ppb/K) of the temperature coefficients observed for the alphaNH protons of residues 5-17. This conformation contrasted with that obtained for apo-con-G, which was nearly structureless in solution. Docking of Mg2+ into con-G was accomplished by use of the genetic algorithm/molecular dynamics simulation method, employing the NMR-derived Mg2+-loaded structure for initial coordinates in the midpoint calculations. For the 3 Mg2+/con-G model, it was found that binding of one Mg2+ ion is stabilized by oxygen atoms from three gamma-carboxylates of Gla3, Gla4, and Gla7; another Mg2+ is coordinated by two oxygen atoms, one from each of the gamma-carboxylates of Gla7; and a third metal ion through three donor oxygen atoms of gamma-carboxylates from Gla10 and Gla14. As shown from direct metal binding measurements to mutant con-G peptides, these latter two Gla residues probably stabilized the tightest binding Mg2+ ion. Circular dichroism studies of these same peptide variants demonstrated that all Gla residues contribute to the adoption of the Mg2+-dependent alpha-helical conformation in con-G. The data obtained in this investigation provide a molecular basis for the large conformational alteration observed in apo-con-G as a result of divalent cation binding and allow assessment of the roles of individual Gla residues in defining certain of the structure-function properties of con-G.
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Affiliation(s)
- Z Chen
- Biomolecular NMR Laboratory and the Montreal Joint Center for Structural Biology, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
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15125
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DEAN R. WHEELER RICHARD L. ROWLEY. Shear viscosity of polar liquid mixtures via non-equilibrium molecular dynamics: water, methanol, and acetone. Mol Phys 1998. [DOI: 10.1080/002689798168060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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15126
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Procacci P, Marchi M, Martyna GJ. Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems. J Chem Phys 1998. [DOI: 10.1063/1.476326] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15127
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Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential. J Chem Phys 1998. [DOI: 10.1063/1.476320] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15128
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Ceccarelli M, Marchi M. Molecular dynamics simulation of POPC at low hydration near the liquid crystal phase transition. Biochimie 1998; 80:415-9. [PMID: 9782382 DOI: 10.1016/s0300-9084(00)80009-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report results of a preliminary molecular dynamics study of a 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) bilayer at low hydration (5% in weight). Our results suggest a gel phase structure where the oleic chain is bent recalling the crystalline oleic acid structure. We have also found a discontinuity in the volume/temperature curve which might be related to the gel to liquid crystal phase transition in POPC.
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Affiliation(s)
- M Ceccarelli
- Centre Européen de Calcul Atomique et Moleculaire (CECAM), Ecole Normale Superieure de Lyon, France
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15129
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Abstract
The growing amount of high quality molecular dynamics simulations generated using the latest methodological developments and force fields has led to a sharper understanding of the forces underlying the dynamics of biomolecular systems, as well as to stimulating insights into the structure and catalysis of nucleic acids. It is now clear that inclusion of long-range electrostatic interactions and of the aqueous and ionic environment is necessary for producing realistic and accurate simulations. Yet, many papers hint at a force field and protocol dependence of the results and thus contain the seeds for the future improvements that will be necessary for deepening our understanding of recognition phenomena and folding of nucleic acids.
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Affiliation(s)
- P Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, Strasbourg, France.
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15130
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Warder SE, Prorok M, Chen Z, Li L, Zhu Y, Pedersen LG, Ni F, Castellino FJ. The roles of individual gamma-carboxyglutamate residues in the solution structure and cation-dependent properties of conantokin-T. J Biol Chem 1998; 273:7512-22. [PMID: 9516452 DOI: 10.1074/jbc.273.13.7512] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the Ca2+-loaded conantokin-T (con-T), a gamma-carboxyglutamate (Gla)-containing 21-residue peptide (NH2-G1EgammagammaY5QKMLgamma10NLRgammaA15EVKKN20A-CONH2,gam ma = Gla), has been elucidated by use of distance geometry calculations with experimental distances derived from two-dimensional 1H NMR spectroscopy. An end-to-end alpha-helix was the dominant conformation in solution, similar to that of apo-con-T, except that reorientation of several side chains occurred in the Ca2+-coordinated complex. The most notable examples of this were those of Gla10 and Gla14, which were more optimally positioned for complexation with Ca2+. In addition to the stabilization offered to the alpha-helix by Ca2+ binding, hydrophobic clustering of the side chains of Tyr5, Met8, Leu9, and Leu12, and ionic interactions between Lys7 and Gla3/Gla10 and between Arg13 and Gla14, along with hydrogen bonding between Gln6 and Gla10, were among the side chain interactions likely playing a significant role in maintenance of the alpha-helical conformation. Docking of Ca2+ in the con-T structure was accomplished using genetic algorithm-molecular dynamics simulation approaches. The results showed that one Ca2+ ion is most likely coordinated by four side chain oxygen atoms, two each from Gla10 and Gla14. Another bound Ca2+ ion has as its donor sites three oxygen atoms, two from Gla3 and one from Gln6. To examine the functional roles of the individual Gla residues, a series of variant peptides have been synthesized with Ala substituted for each Gla residue, and several properties of the resulting variants have been examined. The data obtained demonstrated the importance of Gla10 and Gla14 in stabilizing binding of the highest affinity Ca2+ site and in governing the conformational change induced by Ca2+. The critical nature of Gla3 and Gla4 in inhibition of the spermine-induced potentiation of the binding of MK-801 to open ion channels of the N-methyl-D-aspartate receptor was established, as well as the role of Gla4 in stabilizing the apo-con-T alpha-helical conformation.
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Affiliation(s)
- S E Warder
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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15131
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Meller J, Elber R. Computer simulations of carbon monoxide photodissociation in myoglobin: structural interpretation of the B states. Biophys J 1998; 74:789-802. [PMID: 9533692 PMCID: PMC1302560 DOI: 10.1016/s0006-3495(98)74004-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The early diffusion processes of a photodissociated ligand (carbon monoxide) in sperm whale myoglobin and its Phe29 mutant are studied computationally. An explicit solvent model is employed in which the protein is embedded in a box of at least 2300 water molecules. Electrostatic interactions are accounted for by using the particle mesh Ewald. Two hundred seventy molecular dynamics trajectories are computed for 10 ps. Different models of solvation and the ligand, and their influence on the diffusion are examined. The two B states of the CO are identified as "docking" sites in the heme pocket. The sites have a similar angle with respect to the heme normal, but differ in the orientation in the plane. The computational detection of the B states is stable under a reasonable variation of simulation conditions. However, in some trajectories only one of the states is observed. It is therefore necessary to use extensive simulation data to probe these states. Comparison to diffraction experiments and spectroscopy is performed. The shape of the experimental infrared spectra is computed. The overall linewidth is in an agreement with experiment. The contributions to the linewidth (van der Waals and electrostatic interactions) are discussed.
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Affiliation(s)
- J Meller
- Department of Physical Chemistry, The Fritz Haber Research Center, The Hebrew University, Givat Ram, Jerusalem, Israel
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15132
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15133
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Procacci P, Darden TA, Paci E, Marchi M. ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19971130)18:15<1848::aid-jcc2>3.0.co;2-o] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15134
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Abstract
Molecular dynamics simulations reveal that, in C3'-endo sugar puckers, only three orientations are accessible to the 2'-hydroxyl groups distinctive of RNA molecules: towards (i) the O3', (ii) the O4' of the same sugar, and (iii) the shallow groove base atoms. In the rarer C2'-endo sugar puckers, orientations towards the O3' atom of the same sugar are strongly favoured. Surprisingly, in helical regions, the frequently suggested intra-strand O2'-H(n)...O4'(n+1) interaction is not found. This observation led to the detection of an axial C-H...O interaction between the C2'-H2'(n) group and the O4'(n+1) atom contributing to the stabilization of RNA helical regions. Subsequent analysis of crystallographic structures of both RNA and A-DNA helices fully supports this finding. Specific hydration patterns are also thought to play a significant role in the stabilization of RNA structures. In the shallow groove of RNA, known as a favourable RNA or protein-binding region, three well-defined hydration sites are located around the O2' atom. These hydration sites, occupied by water molecules exchanging with the bulk, constitute, after dehydration, anchor points for specific interactions between RNA and nucleic acids, proteins or drugs. Therefore, the fact that the 2'-hydroxyl group is not monopolised by axial stabilization, together with its water-like behaviour, facilitates complex formation involving RNA helical regions.
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Affiliation(s)
- P Auffinger
- Modélisations et Simulations des Acides Nucléiques UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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15135
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Tieleman DP, Marrink SJ, Berendsen HJ. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1331:235-70. [PMID: 9512654 DOI: 10.1016/s0304-4157(97)00008-7] [Citation(s) in RCA: 557] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- D P Tieleman
- Department of BioPhys. Chem., University of Groningen, The Netherlands.
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15136
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Eichinger M, Grubm�ller H, Heller H, Tavan P. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19971115)18:14<1729::aid-jcc3>3.0.co;2-m] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15137
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Eichinger M, Grubm�ller H, Heller H, Tavan P. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19971115)18:14%3c1729::aid-jcc3%3e3.0.co;2-m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15138
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Cheatham TE, Kollman PA. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). Structure 1997; 5:1297-311. [PMID: 9351805 DOI: 10.1016/s0969-2126(97)00282-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Duplex DNA is more than a simple information carrier. The sequence-dependent structure and its inherent deformability, in concert with the subtle modulating effects of the environment, play a crucial role in the regulation and packaging of DNA. Recent advances in force field and simulation methodologies allow molecular dynamics simulations to now represent the specific effects of the environment. An understanding of the environmental dependence of DNA structure gives insight into how histones are able to package DNA, how various proteins are able to bind and modulate nucleic acid structure and will ultimately aid the design of molecules to package DNA for more effective gene therapy. RESULTS Molecular dynamics simulations of d[ACCCGCGGGT]2 in solution in the presence of hexaamminecobalt(III) [Co(NH3)6(3+)] show stabilization of A-DNA and spontaneous B-DNA to A-DNA transitions, which is consistent with experimental results from NMR and Raman spectroscopic and X-ray crystallographic studies. In the absence of Co(NH3)6(3+), A-DNA to B-DNA transitions are observed instead. In addition to their interaction with the guanines in the major groove, Co(NH3)6(3+) ions bridge opposing strands in the bend across the major groove, probably stabilizing A-DNA. CONCLUSIONS The simulation methods and force fields have advanced to a sufficient level that some representation of the environment can be seen in nanosecond length molecular dynamics simulations. These simulations suggest that, in addition to the general explanation of A-DNA stabilization by dehydration, hydration and ion association in the major groove stabilize A-DNA.
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Affiliation(s)
- T E Cheatham
- Division of Computer Research and Technology, National Institutes of Health, Bethesda, MD 20892-5626, USA
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15139
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Duan Y, Wilkosz P, Crowley M, Rosenberg JM. Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration. J Mol Biol 1997; 272:553-72. [PMID: 9325112 DOI: 10.1006/jmbi.1997.1247] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A molecular dynamics simulation of the dodecamer duplex d(CGCGAATTCGCG) using the particle mesh Ewald sum assumed a B-conformation remarkably close to the observed X-ray structure. The Ewald summation method effectively eliminates the usual "cut-off" of long-range interactions and allowed us to evaluate the full effect of the electrostatic forces. This simulation showed remarkable agreement with the Dickerson X-ray structure in both average structure and B-factors; within the EcoRI site itself, the rms deviation between the average theoretical and observed structures was 1.1 A. The width of the minor groove fluctuated between a wide and narrow configuration with the latter corresponding closely to the X-ray structure. The simulation also suggested a strong sequence-dependent signature on the minor groove width in both wide and narrow conformers. Hydration shells in both the major and minor grooves were observed. The "spine of hydration" in the minor groove was clear. In the major groove the first hydration shell appears to be a ribbon-like structure that reproduces the principal features of observed X-ray structures; subtle variations of this hydration pattern suggest sequence dependencies. Sequence-dependent features were also examined for helical and other geometric parameters. The successful reproduction of many experimentally observed fine structural features shows that the Ewald summation significantly improves the fidelity of the calculations.
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Affiliation(s)
- Y Duan
- Department of Biological Sciences and W. M. Keck Center for Advanced Training in Computational Biology Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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15140
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Samuelson S, Tobias DJ, Martyna GJ. Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters, and Bulk Water. J Phys Chem B 1997. [DOI: 10.1021/jp9704269] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. Samuelson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001
| | - D. J. Tobias
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-0001
| | - G. J. Martyna
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001
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15141
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Cheatham TE, Crowley MF, Fox T, Kollman PA. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc Natl Acad Sci U S A 1997; 94:9626-30. [PMID: 9275173 PMCID: PMC23237 DOI: 10.1073/pnas.94.18.9626] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Advances in computer power, methodology, and empirical force fields now allow routine "stable" nanosecond-length molecular dynamics simulations of DNA in water. The accurate representation of environmental influences on structure remains a major, unresolved issue. In contrast to simulations of A-DNA in water (where an A-DNA to B-DNA transition is observed) and in pure ethanol (where disruption of the structure is observed), A-DNA in approximately 85% ethanol solution remains in a canonical A-DNA geometry as expected. The stabilization of A-DNA by ethanol is likely due to disruption of the spine of hydration in the minor groove and the presence of ion-mediated interhelical bonds and extensive hydration across the major groove.
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Affiliation(s)
- T E Cheatham
- Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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15142
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Gao J, Alhambra C. A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations. J Chem Phys 1997. [DOI: 10.1063/1.474465] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15143
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Miller JL, Kollman PA. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J Mol Biol 1997; 270:436-50. [PMID: 9237909 DOI: 10.1006/jmbi.1997.1113] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report on the results of five independent and unrestrained molecular dynamics simulations of an RNA tetraloop, r(GGACUUCGGUCC), and its related structures with the loop UUCG sugars changed to deoxyribose. Two separate NMR structures have been reported for the loop portion of this molecule, with the second refinement resulting in a slightly different and more accurate conformation for the loop. The root-mean-square deviation (RMSd) between the two NMR structures, for the loop portions only, is 2.5 A. Our simulations, starting from the two NMR structures, demonstrate that this tetraloop is a very stable and rigid structure with both nanosecond length simulations staying very close to the initial structures. Additionally, both simulations preserved most, if not all, of the NMR-derived interactions and violated very few of the nuclear Overhauser effect (NOE)-derived distances used in the structure refinements. However, when the two NMR structures were simulated with deoxyriboses in the loops instead of the native riboses, the flexibility of the systems increased and we observed a conversion from the incorrect to the correct loop conformation in the simulation which started in the incorrect loop conformation. When the riboses were subsequently re-introduced back into the structure which underwent the conversion, the agreement between this simulation and the one starting from the correct NMR structure was a remarkably low 0.5 A, demonstrating an almost complete convergence from the incorrect to the correct structure using unrestrained molecular dynamics.
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Affiliation(s)
- J L Miller
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, 94143-0446, USA
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15144
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Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators. J Chem Phys 1997. [DOI: 10.1063/1.474115] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15145
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Auffinger P, Westhof E. RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin. J Mol Biol 1997; 269:326-41. [PMID: 9199403 DOI: 10.1006/jmbi.1997.1022] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.
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Affiliation(s)
- P Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS Modélisations et Simulations des Acides Nucléiques, UPR 9002, Strasbourg, France.
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15146
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Berne BJ, Straub JE. Novel methods of sampling phase space in the simulation of biological systems. Curr Opin Struct Biol 1997; 7:181-9. [PMID: 9094324 DOI: 10.1016/s0959-440x(97)80023-1] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
New advances in molecular dynamics and Monte Carlo simulations have led to impressive increases in the speed of sampling phase space for complex biological systems. These methods have been combined with new fast algorithms for computing long range electrostatic interactions for new polarizable force fields. In addition, new methods for sampling low energy molecular conformations allow the rapid determination of thermodynamically dominant regions on the potential-energy surface. Accurate measures of the rate of phase-space sampling should allow both the optimization and the comparison of methods for a particular problem of interest.
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Affiliation(s)
- B J Berne
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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15147
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Affiliation(s)
- Matteo Ceccarelli
- Section de Biophysique des Protéines et des Membranes, DBCM, DSV, CEA, Centre d'Études, Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Massimo Marchi
- Section de Biophysique des Protéines et des Membranes, DBCM, DSV, CEA, Centre d'Études, Saclay, 91191 Gif-sur-Yvette Cedex, France
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15148
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Sorescu DC, Rice BM, Thompson DL. Intermolecular Potential for the Hexahydro-1,3,5-trinitro-1,3,5-s-triazine Crystal (RDX): A Crystal Packing, Monte Carlo, and Molecular Dynamics Study. J Phys Chem B 1997. [DOI: 10.1021/jp9624865] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dan C. Sorescu
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, and The U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005
| | - Betsy M. Rice
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, and The U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005
| | - Donald L. Thompson
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, and The U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005
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15149
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Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR. Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9614658] [Citation(s) in RCA: 341] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Scott E. Feller
- Biophysics Laboratory, Center for Biologics Evaluation & Research, Food & Drug Administration, Rockville, Maryland 20852-1448
| | - Richard W. Pastor
- Biophysics Laboratory, Center for Biologics Evaluation & Research, Food & Drug Administration, Rockville, Maryland 20852-1448
| | - Atipat Rojnuckarin
- Department of Chemical Engineering, University of WisconsinMadison, Madison Wisconsin 53706
| | - Stephen Bogusz
- Department of Gastroenterology, Walter Reed Army Institute of Research, Washington, DC 20307
| | - Bernard R. Brooks
- Laboratory of Structural Biology, Division of Computer Research & Technology, National Institutes of Health, Bethesda, Maryland 20892
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15150
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Procacci P, Darden T, Marchi M. A Very Fast Molecular Dynamics Method To Simulate Biomolecular Systems with Realistic Electrostatic Interactions. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp960295w] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piero Procacci
- Centre Européen de Calcul Atomique et Moleculaire (CECAM), Ecole Normale Superieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Tom Darden
- National Institute of Environmental Health, Sciences Research Triangle Park, North Carolina 27709
| | - Massimo Marchi
- Section de Biophysique des Protéines et des Membranes, DBCM, DSV, CEA, Centre d'Études, Saclay, 91191 Gif-sur-Yvette Cedex, France
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